6-45735042-C-T

Variant names:

• chr6-45735042-C-T
• rs321320

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 0.745 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.574 AC: 23785 AN: 41440

American (AMR) AF: 0.810 AC: 12377 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2707 AN: 3468

East Asian (EAS) AF: 0.981 AC: 5087 AN: 5186

South Asian (SAS) AF: 0.838 AC: 4036 AN: 4816

European-Finnish (FIN) AF: 0.865 AC: 9147 AN: 10576

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53764 AN: 67974

Other (OTH) AF: 0.753 AC: 1592 AN: 2114

Alfa AF: 0.778 Hom.: 191186

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
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs321320; hg19: chr6-45702779;