8-9938679-T-C

Variant names:

• chr8-9938679-T-C
• rs615171
• ENST00000843628.1:n.98-3543T>C

Variant summary

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

The ENST00000843628.1(ENSG00000309740):​n.98-3543T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,184 control chromosomes in the GnomAD database, including 50,303 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 0.81 (50303 hom., cov: 32)
• Consequence: ENSG00000309740 ENST00000843628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127
• Publications: 8 publications found

Genes affected

ENSG00000309740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843628.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309740	ENST00000843628.1		n.98-3543T>C		intron	N/A
	ENSG00000309740	ENST00000843629.1		n.175-3543T>C		intron	N/A
	ENSG00000309740	ENST00000843630.1		n.170-3543T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123532 AN: 152066 Hom.: 50270 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.812 AC: 123617 AN: 152184 Hom.: 50303 Cov.: 32 AF XY: 0.810 AC XY: 60249 AN XY: 74410

African (AFR) AF: 0.840 AC: 34887 AN: 41522

American (AMR) AF: 0.792 AC: 12107 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.840 AC: 2915 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3902 AN: 5180

South Asian (SAS) AF: 0.831 AC: 4006 AN: 4820

European-Finnish (FIN) AF: 0.755 AC: 7994 AN: 10594

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55036 AN: 68004

Other (OTH) AF: 0.835 AC: 1763 AN: 2112

Alfa AF: 0.814 Hom.: 204053

Bravo AF: 0.816

Asia WGS AF: 0.806 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.55
PhyloP100		-0.13

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs615171;

hg19: chr8-9796189;