rs7185923

Variant names:

• chr16-51211576-T-C
• rs7185923
• ENST00000642450.1:n.350+22567T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-51211576-T-C
• chr16-51211576-T-G

Variant summary

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

The ENST00000642450.1(ENSG00000285367):​n.350+22567T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,062 control chromosomes in the GnomAD database, including 14,357 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 0.39 (14357 hom., cov: 32)
• Consequence: ENSG00000285367 ENST00000642450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 3 publications found

Genes affected

ENSG00000285367 (HGNC:58539):

ENSG00000287256 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.599 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
ENSG00000285367	ENST00000642450.1	n.350+22567T>C		intron_variant	Intron 2 of 3
ENSG00000285367	ENST00000643626.1	n.51+59401T>C		intron_variant	Intron 1 of 6
ENSG00000285367	ENST00000644069.1	n.56-35238T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59861 AN: 151944 Hom.: 14357 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.394 AC: 59858 AN: 152062 Hom.: 14357 Cov.: 32 AF XY: 0.403 AC XY: 29978 AN XY: 74326

African (AFR) AF: 0.0998 AC: 4144 AN: 41522

American (AMR) AF: 0.482 AC: 7359 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1559 AN: 3472

East Asian (EAS) AF: 0.564 AC: 2914 AN: 5164

South Asian (SAS) AF: 0.618 AC: 2975 AN: 4814

European-Finnish (FIN) AF: 0.562 AC: 5927 AN: 10552

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33376 AN: 67950

Other (OTH) AF: 0.431 AC: 907 AN: 2106

Alfa AF: 0.409 Hom.: 11278

Bravo AF: 0.369

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.50
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs7185923; hg19: chr16-51245487;