rs2365465

Variant names:

• chr1-61667440-T-C
• rs2365465

Your query was ambiguous. Multiple possible variants found:

• chr1-61667440-T-C
• chr1-61667440-T-G

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 0.118 in 151,992 control chromosomes in the GnomAD database, including 1,122 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 0.12 (1122 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17969 AN: 151874 Hom.: 1120 Cov.: 31

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.118 AC: 17984 AN: 151992 Hom.: 1122 Cov.: 31 AF XY: 0.117 AC XY: 8663 AN XY: 74282

African (AFR) AF: 0.136 AC: 5639 AN: 41470

American (AMR) AF: 0.107 AC: 1641 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3468

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5172

South Asian (SAS) AF: 0.0426 AC: 205 AN: 4810

European-Finnish (FIN) AF: 0.116 AC: 1226 AN: 10544

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.123 AC: 8361 AN: 67944

Other (OTH) AF: 0.129 AC: 274 AN: 2116

Alfa AF: 0.123 Hom.: 2210

Bravo AF: 0.119

Asia WGS AF: 0.0360 AC: 125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.20
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2365465; hg19: chr1-62133112;