ENST00000776949.1:n.631G>A

Variant names:

• chr8-2173969-G-A
• rs936553
• ENST00000776949.1:n.631G>A

Variant summary

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

The ENST00000776949.1(ENSG00000288782):​n.631G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,598 control chromosomes in the GnomAD database, including 4,420 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 0.24 (4420 hom., cov: 31)
• Consequence: ENSG00000288782 ENST00000776949.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.654
• Publications: 0 publications found

Genes affected

ENSG00000288782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=2.199).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776949.1. 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
	ENSG00000288782	ENST00000776949.1		n.631G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000288782	ENST00000776950.1		n.748G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000288782	ENST00000685917.3		n.113-9030G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36652 AN: 151482 Hom.: 4417 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.242 AC: 36669 AN: 151598 Hom.: 4420 Cov.: 31 AF XY: 0.241 AC XY: 17862 AN XY: 74106

African (AFR) AF: 0.256 AC: 10595 AN: 41316

American (AMR) AF: 0.301 AC: 4574 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3466

East Asian (EAS) AF: 0.142 AC: 731 AN: 5146

South Asian (SAS) AF: 0.112 AC: 540 AN: 4810

European-Finnish (FIN) AF: 0.250 AC: 2625 AN: 10512

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16008 AN: 67834

Other (OTH) AF: 0.229 AC: 481 AN: 2100

Alfa AF: 0.139 Hom.: 229

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	2.2
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs936553;