1-161493708-G-A

Variant names:

• chr1-161493708-G-A
• rs6427595
• XR_922214.3:n.1903+89G>A

Variant summary

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

The XR_922214.3(LOC105371473):​n.1903+89G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,146 control chromosomes in the GnomAD database, including 42,246 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 0.74 (42246 hom., cov: 32)
• Consequence: LOC105371473 XR_922214.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 7 publications found

Genes affected

LOC105371473 (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 (AMR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371473	XR_922214.3	n.1903+89G>A		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112180 AN: 152026 Hom.: 42219 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.738 AC: 112264 AN: 152146 Hom.: 42246 Cov.: 32 AF XY: 0.733 AC XY: 54464 AN XY: 74352

African (AFR) AF: 0.755 AC: 31344 AN: 41498

American (AMR) AF: 0.770 AC: 11774 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2809 AN: 3472

East Asian (EAS) AF: 0.282 AC: 1458 AN: 5174

South Asian (SAS) AF: 0.542 AC: 2608 AN: 4812

European-Finnish (FIN) AF: 0.725 AC: 7672 AN: 10582

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52151 AN: 67994

Other (OTH) AF: 0.730 AC: 1540 AN: 2110

Alfa AF: 0.710 Hom.: 4817

Bravo AF: 0.746

Asia WGS AF: 0.454 AC: 1585 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	3.1
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6427595; hg19: chr1-161463498;