rs410377

Variant names:

• chr6-160313903-G-C
• rs410377

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 0.464 in 152,074 control chromosomes in the GnomAD database, including 16,834 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 0.46 (16834 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.53 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: 0.463 AC: 70429 AN: 151954 Hom.: 16822 Cov.: 33

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.464 AC: 70489 AN: 152074 Hom.: 16834 Cov.: 33 AF XY: 0.464 AC XY: 34476 AN XY: 74352

African (AFR) AF: 0.364 AC: 15105 AN: 41478

American (AMR) AF: 0.431 AC: 6584 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1387 AN: 5166

South Asian (SAS) AF: 0.412 AC: 1988 AN: 4824

European-Finnish (FIN) AF: 0.530 AC: 5604 AN: 10570

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.534 AC: 36323 AN: 67970

Other (OTH) AF: 0.485 AC: 1025 AN: 2112

Alfa AF: 0.499 Hom.: 2387

Bravo AF: 0.457

Asia WGS AF: 0.351 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.26
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs410377; hg19: chr6-160734935;