1-221432490-A-T

Variant names:

• chr1-221432490-A-T
• rs10495163
• XR_922621.2:n.623-37652A>T

Variant summary

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

The XR_922621.2(LOC105372932):​n.623-37652A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 152,040 control chromosomes in the GnomAD database, including 11,750 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 (11750 hom., cov: 32)
• Consequence: LOC105372932 XR_922621.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 1 publications found

Genes affected

LOC105372932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372932	XR_922621.2	n.623-37652A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59264 AN: 151922 Hom.: 11737 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.390 AC: 59308 AN: 152040 Hom.: 11750 Cov.: 32 AF XY: 0.389 AC XY: 28875 AN XY: 74322

African (AFR) AF: 0.318 AC: 13169 AN: 41444

American (AMR) AF: 0.398 AC: 6089 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1482 AN: 5170

South Asian (SAS) AF: 0.371 AC: 1790 AN: 4822

European-Finnish (FIN) AF: 0.440 AC: 4647 AN: 10554

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29775 AN: 67976

Other (OTH) AF: 0.396 AC: 836 AN: 2110

Alfa AF: 0.411 Hom.: 1638

Bravo AF: 0.384

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.024
DANN	Benign	0.76
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs10495163; hg19: chr1-221605832; COSMIC: COSV50456249;