rs7722022

Variant names:

• chr5-173507895-C-A
• rs7722022
• ENST00000827042.1:n.446+1523C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-173507895-C-A
• chr5-173507895-C-G
• chr5-173507895-C-T

Variant summary

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

The ENST00000827042.1(ENSG00000253968):​n.446+1523C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,954 control chromosomes in the GnomAD database, including 12,003 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 0.40 (12003 hom., cov: 31)
• Consequence: ENSG00000253968 ENST00000827042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 9 publications found

Genes affected

ENSG00000253968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1	n.3056+305C>A		intron_variant	Intron 14 of 14
LOC105377732	XR_007059057.1	n.4116+305C>A		intron_variant	Intron 17 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253968	ENST00000827042.1	n.446+1523C>A		intron_variant	Intron 2 of 2
ENSG00000253968	ENST00000827044.1	n.374+1523C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60003 AN: 151836 Hom.: 11970 Cov.: 31

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.395 AC: 60091 AN: 151954 Hom.: 12003 Cov.: 31 AF XY: 0.399 AC XY: 29606 AN XY: 74278

African (AFR) AF: 0.387 AC: 16018 AN: 41436

American (AMR) AF: 0.480 AC: 7338 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1520 AN: 5164

South Asian (SAS) AF: 0.419 AC: 2015 AN: 4810

European-Finnish (FIN) AF: 0.388 AC: 4101 AN: 10564

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26538 AN: 67916

Other (OTH) AF: 0.421 AC: 888 AN: 2110

Alfa AF: 0.365 Hom.: 3936

Bravo AF: 0.401

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.84
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs7722022; hg19: chr5-172934898; COSMIC: COSV60232117;