rs936553

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr8-2173969-G-A
• chr8-2173969-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377781	XR_941356.3	n.107+17186G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288782	ENST00000776949.1	n.631G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000288782	ENST00000776950.1	n.748G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000288782	ENST00000685917.3	n.113-9030G>A		intron_variant	Intron 1 of 1

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 v4.3

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; hg19: -;