1-201265958-A-G

Variant names:

• chr1-201265958-A-G
• rs2365642

Variant summary

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

The variant allele was found at a frequency of 0.408 in 151,950 control chromosomes in the GnomAD database, including 14,352 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 0.41 (14352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61858 AN: 151832 Hom.: 14312 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.408 AC: 61956 AN: 151950 Hom.: 14352 Cov.: 32 AF XY: 0.411 AC XY: 30494 AN XY: 74258

African (AFR) AF: 0.649 AC: 26880 AN: 41434

American (AMR) AF: 0.334 AC: 5106 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1222 AN: 5172

South Asian (SAS) AF: 0.352 AC: 1693 AN: 4814

European-Finnish (FIN) AF: 0.400 AC: 4223 AN: 10550

Middle Eastern (MID) AF: 0.397 AC: 115 AN: 290

European-Non Finnish (NFE) AF: 0.302 AC: 20527 AN: 67918

Other (OTH) AF: 0.369 AC: 779 AN: 2112

Alfa AF: 0.329 Hom.: 4631

Bravo AF: 0.411

Asia WGS AF: 0.354 AC: 1231 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		0.063

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2365642;

hg19: chr1-201235086;

COSMIC: COSV107160293;