6-30934756-T-C

Variant names:

• chr6-30934756-T-C
• rs2844650
• ENST00000850875.1:c.52+82T>C

Variant summary

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

The ENST00000850875.1(ENSG00000310558):​c.52+82T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 398,540 control chromosomes in the GnomAD database, including 168,088 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 0.93 (65788 hom., cov: 31)
  • Exomes 𝑓: 0.91 (102300 hom.)
• Consequence: ENSG00000310558 ENST00000850875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 16 publications found

Genes affected

ENSG00000310558 (HGNC:):

SFTA2 (HGNC:18386): (surfactant associated 2) Predicted to be located in Golgi apparatus; extracellular region; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310558	ENST00000850875.1	c.52+82T>C		intron_variant	Intron 1 of 2			ENSP00000520959.1
SFTA2	ENST00000634371.2	n.514-2961A>G		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.929 AC: 141284 AN: 152140 Hom.: 65727 Cov.: 31

Gnomad AFR AF: 0.976

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.942

GnomAD4 exome AF: 0.911 AC: 224265 AN: 246282 Hom.: 102300 AF XY: 0.910 AC XY: 113517 AN XY: 124802

African (AFR) AF: 0.976 AC: 7006 AN: 7178

American (AMR) AF: 0.955 AC: 7097 AN: 7432

Ashkenazi Jewish (ASJ) AF: 0.966 AC: 8925 AN: 9240

East Asian (EAS) AF: 0.956 AC: 21886 AN: 22888

South Asian (SAS) AF: 0.968 AC: 2934 AN: 3030

European-Finnish (FIN) AF: 0.896 AC: 18650 AN: 20812

Middle Eastern (MID) AF: 0.962 AC: 1245 AN: 1294

European-Non Finnish (NFE) AF: 0.895 AC: 141379 AN: 158044

Other (OTH) AF: 0.925 AC: 15143 AN: 16364

GnomAD4 genome AF: 0.929 AC: 141404 AN: 152258 Hom.: 65788 Cov.: 31 AF XY: 0.929 AC XY: 69171 AN XY: 74436

African (AFR) AF: 0.976 AC: 40563 AN: 41560

American (AMR) AF: 0.942 AC: 14410 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.966 AC: 3355 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5085 AN: 5164

South Asian (SAS) AF: 0.973 AC: 4691 AN: 4822

European-Finnish (FIN) AF: 0.895 AC: 9493 AN: 10604

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60670 AN: 68018

Other (OTH) AF: 0.943 AC: 1994 AN: 2114

Alfa AF: 0.907 Hom.: 188599

Bravo AF: 0.936

Asia WGS AF: 0.970 AC: 3375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.99
DANN	Benign	0.59
PhyloP100		-0.72
PromoterAI		-0.0078	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2844650; hg19: chr6-30902533;