rs1065780

Variant names:

• chr7-45888078-G-A
• rs1065780

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 0.389 in 151,954 control chromosomes in the GnomAD database, including 11,731 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 0.39 (11731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 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: 0.389 AC: 59090 AN: 151836 Hom.: 11710 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.389 AC: 59143 AN: 151954 Hom.: 11731 Cov.: 32 AF XY: 0.385 AC XY: 28555 AN XY: 74252

African (AFR) AF: 0.421 AC: 17445 AN: 41426

American (AMR) AF: 0.372 AC: 5684 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1303 AN: 3458

East Asian (EAS) AF: 0.534 AC: 2746 AN: 5146

South Asian (SAS) AF: 0.207 AC: 995 AN: 4818

European-Finnish (FIN) AF: 0.332 AC: 3493 AN: 10536

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26300 AN: 67972

Other (OTH) AF: 0.399 AC: 843 AN: 2112

Alfa AF: 0.388 Hom.: 15351

Bravo AF: 0.401

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.065
DANN	Benign	0.60
PhyloP100		-2.3
PromoterAI		-0.014	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1065780; hg19: chr7-45927677;