7-19939811-A-G

Variant names:

• chr7-19939811-A-G
• rs10486376
• ENST00000415499.6:n.544-8513T>C

Variant summary

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

The ENST00000415499.6(ENSG00000243004):​n.544-8513T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0682 in 152,036 control chromosomes in the GnomAD database, including 833 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 0.068 (833 hom., cov: 32)
• Consequence: ENSG00000243004 ENST00000415499.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 1 publications found

Genes affected

ENSG00000243004 (HGNC:58196):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MACC1-OT1	NR_110114.1	n.543-20551T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000243004	ENST00000415499.6	n.544-8513T>C		intron_variant	Intron 5 of 5	3
ENSG00000243004	ENST00000435968.5	n.491-20551T>C		intron_variant	Intron 5 of 5	2
ENSG00000243004	ENST00000437191.6	n.526-8513T>C		intron_variant	Intron 5 of 7	2

Frequencies

GnomAD3 genomes AF: 0.0679 AC: 10321 AN: 151918 Hom.: 826 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.0891

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.0431

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0682 AC: 10365 AN: 152036 Hom.: 833 Cov.: 32 AF XY: 0.0692 AC XY: 5144 AN XY: 74344

African (AFR) AF: 0.158 AC: 6529 AN: 41434

American (AMR) AF: 0.0227 AC: 347 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0188 AC: 65 AN: 3462

East Asian (EAS) AF: 0.351 AC: 1808 AN: 5150

South Asian (SAS) AF: 0.0888 AC: 428 AN: 4820

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10596

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0126 AC: 855 AN: 67988

Other (OTH) AF: 0.0460 AC: 97 AN: 2108

Alfa AF: 0.0402 Hom.: 63

Bravo AF: 0.0727

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.72
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs10486376; hg19: chr7-19979434;