rs6672903

Variant names:

• chr1-119456589-A-G
• rs6672903
• ENST00000632456.2:n.769-21442T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-119456589-A-G
• chr1-119456589-A-T

Variant summary

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

The ENST00000632456.2(ENSG00000293080):​n.769-21442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,100 control chromosomes in the GnomAD database, including 26,666 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 0.57 (26666 hom., cov: 33)
• Consequence: ENSG00000293080 ENST00000632456.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 6 publications found

Genes affected

ENSG00000293080 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293080	ENST00000632456.2	n.769-21442T>C		intron_variant	Intron 6 of 6	6
ENSG00000293080	ENST00000756944.1	n.340-21442T>C		intron_variant	Intron 3 of 3
ENSG00000293080	ENST00000756945.1	n.519-21442T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86795 AN: 151982 Hom.: 26636 Cov.: 33

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.571 AC: 86886 AN: 152100 Hom.: 26666 Cov.: 33 AF XY: 0.573 AC XY: 42616 AN XY: 74332

African (AFR) AF: 0.812 AC: 33727 AN: 41526

American (AMR) AF: 0.557 AC: 8507 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3470

East Asian (EAS) AF: 0.590 AC: 3050 AN: 5168

South Asian (SAS) AF: 0.506 AC: 2436 AN: 4810

European-Finnish (FIN) AF: 0.523 AC: 5527 AN: 10564

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.446 AC: 30349 AN: 67978

Other (OTH) AF: 0.530 AC: 1117 AN: 2108

Alfa AF: 0.480 Hom.: 76490

Bravo AF: 0.588

Asia WGS AF: 0.584 AC: 2032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.0
DANN	Benign	0.80
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs6672903; hg19: chr1-119999212;