rs7521902

Variant names:

• chr1-22164231-C-A
• rs7521902
• ENST00000725701.1:n.125+735C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-22164231-C-A
• chr1-22164231-C-G
• chr1-22164231-C-T

Variant summary

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

The ENST00000725701.1(ENSG00000294752):​n.125+735C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,158 control chromosomes in the GnomAD database, including 4,217 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 (4217 hom., cov: 32)
• Consequence: ENSG00000294752 ENST00000725701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300
• Publications: 98 publications found

Genes affected

ENSG00000294752 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376850	XR_947057.3	n.154+735C>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294752	ENST00000725701.1	n.125+735C>A		intron_variant	Intron 1 of 3
ENSG00000294752	ENST00000725702.1	n.125+735C>A		intron_variant	Intron 1 of 2
ENSG00000294752	ENST00000725703.1	n.108+735C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33684 AN: 152040 Hom.: 4204 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.222 AC: 33722 AN: 152158 Hom.: 4217 Cov.: 32 AF XY: 0.229 AC XY: 17009 AN XY: 74384

African (AFR) AF: 0.152 AC: 6317 AN: 41514

American (AMR) AF: 0.249 AC: 3808 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2619 AN: 5164

South Asian (SAS) AF: 0.336 AC: 1618 AN: 4818

European-Finnish (FIN) AF: 0.251 AC: 2655 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15644 AN: 67988

Other (OTH) AF: 0.204 AC: 431 AN: 2114

Alfa AF: 0.231 Hom.: 11567

Bravo AF: 0.218

Asia WGS AF: 0.400 AC: 1388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.76
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs7521902; hg19: chr1-22490724; COSMIC: COSV50192719;