rs1661609

Variant names:

• chr7-52685570-T-A
• rs1661609

Your query was ambiguous. Multiple possible variants found:

• chr7-52685570-T-A
• chr7-52685570-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 0.77 in 152,170 control chromosomes in the GnomAD database, including 45,417 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 0.77 (45417 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.836 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: 0.770 AC: 117115 AN: 152052 Hom.: 45371 Cov.: 33

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.770 AC: 117219 AN: 152170 Hom.: 45417 Cov.: 33 AF XY: 0.773 AC XY: 57508 AN XY: 74392

African (AFR) AF: 0.843 AC: 34987 AN: 41502

American (AMR) AF: 0.744 AC: 11385 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3472

East Asian (EAS) AF: 0.710 AC: 3671 AN: 5174

South Asian (SAS) AF: 0.756 AC: 3648 AN: 4828

European-Finnish (FIN) AF: 0.823 AC: 8709 AN: 10586

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49636 AN: 67992

Other (OTH) AF: 0.779 AC: 1645 AN: 2112

Alfa AF: 0.747 Hom.: 5289

Bravo AF: 0.765

Asia WGS AF: 0.740 AC: 2576 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	5.1
DANN	Benign	0.61
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1661609; hg19: chr7-52753265;