rs6983269

Variant names:

• chr8-2741967-C-A
• rs6983269
• ENST00000520024.1:n.176+14474C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-2741967-C-A
• chr8-2741967-C-G
• chr8-2741967-C-T

Variant summary

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

The ENST00000520024.1(ENSG00000253853):​n.176+14474C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,034 control chromosomes in the GnomAD database, including 14,892 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 0.43 (14892 hom., cov: 33)
• Consequence: ENSG00000253853 ENST00000520024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 3 publications found

Genes affected

ENSG00000253853 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520024.1. 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
	LOC105377785	NR_168441.1		n.538+14474C>A		intron	N/A
	LOC105377785	NR_168442.1		n.538+14474C>A		intron	N/A
	LOC105377785	NR_168443.1		n.538+14474C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253853	ENST00000520024.1	TSL:3	n.176+14474C>A		intron	N/A
	ENSG00000253853	ENST00000654515.1		n.531+14474C>A		intron	N/A
	ENSG00000253853	ENST00000670600.1		n.538+14474C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65087 AN: 151916 Hom.: 14878 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.428 AC: 65121 AN: 152034 Hom.: 14892 Cov.: 33 AF XY: 0.434 AC XY: 32231 AN XY: 74306

African (AFR) AF: 0.277 AC: 11477 AN: 41436

American (AMR) AF: 0.590 AC: 9019 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3468

East Asian (EAS) AF: 0.365 AC: 1885 AN: 5170

South Asian (SAS) AF: 0.538 AC: 2593 AN: 4824

European-Finnish (FIN) AF: 0.485 AC: 5115 AN: 10546

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31719 AN: 67988

Other (OTH) AF: 0.453 AC: 954 AN: 2108

Alfa AF: 0.317 Hom.: 846

Bravo AF: 0.430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.1
PhyloP100		0.20

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: rs6983269;

hg19: chr8-2599496;