rs7521536

Variant names:

• chr1-173496126-T-C
• rs7521536
• ENST00000779108.1:n.65+629T>C

Variant summary

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

The ENST00000779108.1(ENSG00000301478):​n.65+629T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,058 control chromosomes in the GnomAD database, including 3,969 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 0.22 (3969 hom., cov: 32)
• Consequence: ENSG00000301478 ENST00000779108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 7 publications found

Genes affected

ENSG00000301478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779108.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301478	ENST00000779108.1		n.65+629T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33382 AN: 151940 Hom.: 3951 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.220 AC: 33453 AN: 152058 Hom.: 3969 Cov.: 32 AF XY: 0.218 AC XY: 16179 AN XY: 74364

African (AFR) AF: 0.298 AC: 12338 AN: 41424

American (AMR) AF: 0.193 AC: 2952 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1613 AN: 5180

South Asian (SAS) AF: 0.117 AC: 567 AN: 4828

European-Finnish (FIN) AF: 0.137 AC: 1449 AN: 10582

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12745 AN: 67980

Other (OTH) AF: 0.215 AC: 454 AN: 2110

Alfa AF: 0.201 Hom.: 10410

Bravo AF: 0.230

Asia WGS AF: 0.214 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.35
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7521536; hg19: chr1-173465265;