6-137916852-C-T

Variant names:

• chr6-137916852-C-T
• rs77000060

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0332 in 152,112 control chromosomes in the GnomAD database, including 95 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 0.033 (95 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0332 (5055/152112) while in subpopulation AFR AF = 0.048 (1991/41496). AF 95% confidence interval is 0.0462. There are 95 homozygotes in GnomAd4. There are 2415 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 95 gene

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: 0.0332 AC: 5046 AN: 151994 Hom.: 95 Cov.: 32

Gnomad AFR AF: 0.0479

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0403

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0283

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0332 AC: 5055 AN: 152112 Hom.: 95 Cov.: 32 AF XY: 0.0325 AC XY: 2415 AN XY: 74356

African (AFR) AF: 0.0480 AC: 1991 AN: 41496

American (AMR) AF: 0.0240 AC: 366 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0403 AC: 140 AN: 3470

East Asian (EAS) AF: 0.0425 AC: 220 AN: 5178

South Asian (SAS) AF: 0.0361 AC: 174 AN: 4822

European-Finnish (FIN) AF: 0.0164 AC: 174 AN: 10602

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0283 AC: 1925 AN: 67958

Other (OTH) AF: 0.0275 AC: 58 AN: 2108

Alfa AF: 0.0162 Hom.: 3

Bravo AF: 0.0338

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.44
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs77000060; hg19: chr6-138237989;