rs6465825

Variant names:

• chr7-77787122-T-C
• rs6465825

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 0.409 in 152,002 control chromosomes in the GnomAD database, including 13,103 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 (13103 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.409 AC: 62048 AN: 151884 Hom.: 13076 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.409 AC: 62132 AN: 152002 Hom.: 13103 Cov.: 31 AF XY: 0.403 AC XY: 29962 AN XY: 74300

African (AFR) AF: 0.493 AC: 20417 AN: 41426

American (AMR) AF: 0.364 AC: 5558 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1673 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1076 AN: 5174

South Asian (SAS) AF: 0.355 AC: 1716 AN: 4828

European-Finnish (FIN) AF: 0.340 AC: 3585 AN: 10550

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26748 AN: 67956

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.395 Hom.: 52050

Bravo AF: 0.408

Asia WGS AF: 0.341 AC: 1185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.93
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs6465825; hg19: chr7-77416439;