rs6996964

Variant names:

• chr8-19766400-C-T
• rs6996964
• ENST00000773374.1:n.342-4247G>A

Variant summary

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

The ENST00000773374.1(ENSG00000300677):​n.342-4247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,954 control chromosomes in the GnomAD database, including 2,355 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 0.14 (2355 hom., cov: 30)
• Consequence: ENSG00000300677 ENST00000773374.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 3 publications found

Genes affected

ENSG00000300677 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000773374.1. 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
	ENSG00000300677	ENST00000773374.1		n.342-4247G>A		intron	N/A
	ENSG00000300677	ENST00000773375.1		n.342-7416G>A		intron	N/A
	ENSG00000300677	ENST00000773376.1		n.317-4247G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20834 AN: 151836 Hom.: 2339 Cov.: 30

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.0539

Gnomad FIN AF: 0.0552

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.137 AC: 20885 AN: 151954 Hom.: 2355 Cov.: 30 AF XY: 0.133 AC XY: 9886 AN XY: 74264

African (AFR) AF: 0.313 AC: 12939 AN: 41320

American (AMR) AF: 0.0908 AC: 1386 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3472

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5184

South Asian (SAS) AF: 0.0533 AC: 257 AN: 4824

European-Finnish (FIN) AF: 0.0552 AC: 584 AN: 10578

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0706 AC: 4800 AN: 67996

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.0913 Hom.: 3905

Bravo AF: 0.148

Asia WGS AF: 0.0570 AC: 202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.49
PhyloP100		-0.056

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: rs6996964;

hg19: chr8-19623911;