rs4659996

Variant names:

• chr1-240682824-G-A
• rs4659996

Your query was ambiguous. Multiple possible variants found:

• chr1-240682824-G-A
• chr1-240682824-G-C
• chr1-240682824-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.557 in 151,956 control chromosomes in the GnomAD database, including 24,435 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 0.56 (24435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.714 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: 0.557 AC: 84563 AN: 151840 Hom.: 24409 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.557 AC: 84638 AN: 151956 Hom.: 24435 Cov.: 32 AF XY: 0.557 AC XY: 41362 AN XY: 74274

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.532

Alfa AF: 0.493 Hom.: 32352

Bravo AF: 0.566

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4659996; hg19: chr1-240846124;