rs6465825

Variant names:

• chr7-77787122-T-C
• rs6465825

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 0.409 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.403

Alfa AF: 0.393 Hom.: 25784

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6465825; hg19: chr7-77416439;