6-135105420-A-T

Variant names:

• chr6-135105420-A-T
• rs4895440

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 0.293 in 151,976 control chromosomes in the GnomAD database, including 6,961 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 0.29 (6961 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.616

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 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: 0.293 AC: 44499 AN: 151858 Hom.: 6939 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.293 AC: 44560 AN: 151976 Hom.: 6961 Cov.: 32 AF XY: 0.290 AC XY: 21565 AN XY: 74270

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.259

Alfa AF: 0.279 Hom.: 770

Bravo AF: 0.293

Asia WGS AF: 0.206 AC: 717 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	1.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4895440; hg19: chr6-135426558; COSMIC: COSV73231474;