6-45735042-C-T

Position:

• chr6-45735042-C-T

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 0.745 in 152,064 control chromosomes in the GnomAD database, including 43,094 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 0.75 (43094 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113202 AN: 151946 Hom.: 43048 Cov.: 31

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.745 AC: 113301 AN: 152064 Hom.: 43094 Cov.: 31 AF XY: 0.753 AC XY: 55978 AN XY: 74344

Gnomad4 AFR AF: 0.574

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.753

Alfa AF: 0.785 Hom.: 91262

Bravo AF: 0.734

Asia WGS AF: 0.888 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.33
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs321320; hg19: chr6-45702779;