rs7546619

Variant names:

• chr1-173057711-G-A
• rs7546619
• ENST00000432694.2:n.666-6162G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-173057711-G-A
• chr1-173057711-G-C
• chr1-173057711-G-T

Variant summary

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

The ENST00000432694.2(ENSG00000224000):​n.666-6162G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,938 control chromosomes in the GnomAD database, including 7,402 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 0.29 (7402 hom., cov: 32)
• Consequence: ENSG00000224000 ENST00000432694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• Publications: 3 publications found

Genes affected

ENSG00000224000 (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 (EAS) allele frequency at 95% confidence interval = 0.764 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
ENSG00000224000	ENST00000432694.2	n.666-6162G>A		intron_variant	Intron 4 of 4	3
ENSG00000224000	ENST00000717048.1	n.324-6162G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43462 AN: 151820 Hom.: 7409 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.286 AC: 43480 AN: 151938 Hom.: 7402 Cov.: 32 AF XY: 0.292 AC XY: 21650 AN XY: 74256

African (AFR) AF: 0.233 AC: 9675 AN: 41438

American (AMR) AF: 0.371 AC: 5662 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1240 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4045 AN: 5158

South Asian (SAS) AF: 0.553 AC: 2667 AN: 4820

European-Finnish (FIN) AF: 0.197 AC: 2077 AN: 10542

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16997 AN: 67960

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.275 Hom.: 10191

Bravo AF: 0.298

Asia WGS AF: 0.612 AC: 2125 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	11
DANN	Benign	0.48
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs7546619; hg19: chr1-173026851;