17-82328303-C-G

Variant names:

• chr17-82328303-C-G
• rs6502097
• NM_003004.3:c.-52-1011G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003004.3(SECTM1):​c.-52-1011G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,134 control chromosomes in the GnomAD database, including 53,335 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.83 (53312 hom., cov: 31)
  • Exomes 𝑓: 0.84 (23 hom.)
• Consequence: SECTM1 NM_003004.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 7 publications found

Genes affected

SECTM1 (HGNC:10707): (secreted and transmembrane 1) This gene encodes a transmembrane and secreted protein with characteristics of a type 1a transmembrane protein. It is found in a perinuclear Golgi-like pattern and thought to be involved in hematopoietic and/or immune system processes. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003004.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SECTM1	NM_003004.3	MANE Select	c.-52-1011G>C		intron	N/A	NP_002995.1	Q8WVN6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SECTM1	ENST00000269389.8	TSL:1 MANE Select	c.-52-1011G>C		intron	N/A	ENSP00000269389.3	Q8WVN6
	SECTM1	ENST00000856795.1		c.-1063G>C		5_prime_UTR	Exon 1 of 4	ENSP00000526854.1
	SECTM1	ENST00000856797.1		c.-75G>C		5_prime_UTR	Exon 1 of 5	ENSP00000526856.1

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126817 AN: 151954 Hom.: 53263 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.820

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.799

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.819

GnomAD4 exome AF: 0.839 AC: 52 AN: 62 Hom.: 23 Cov.: 0 AF XY: 0.848 AC XY: 39 AN XY: 46

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AF: 0.500 AC: 2 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.909 AC: 40 AN: 44

Other (OTH) AF: 0.625 AC: 5 AN: 8

GnomAD4 genome AF: 0.835 AC: 126924 AN: 152072 Hom.: 53312 Cov.: 31 AF XY: 0.836 AC XY: 62149 AN XY: 74330

African (AFR) AF: 0.741 AC: 30746 AN: 41474

American (AMR) AF: 0.799 AC: 12201 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.820 AC: 2845 AN: 3470

East Asian (EAS) AF: 0.848 AC: 4346 AN: 5124

South Asian (SAS) AF: 0.891 AC: 4302 AN: 4826

European-Finnish (FIN) AF: 0.896 AC: 9493 AN: 10596

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.886 AC: 60219 AN: 67992

Other (OTH) AF: 0.822 AC: 1734 AN: 2110

Alfa AF: 0.855 Hom.: 3222

Bravo AF: 0.820

Asia WGS AF: 0.861 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.37
PhyloP100		-2.7
PromoterAI		0.028	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6502097; hg19: chr17-80286179;