chr10-44665661-C-T

Variant names:

• chr10-44665661-C-T
• rs1480597

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 0.13 in 152,202 control chromosomes in the GnomAD database, including 1,508 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 0.13 (1508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.935
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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: 0.131 AC: 19854 AN: 152084 Hom.: 1508 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0514

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.130 AC: 19859 AN: 152202 Hom.: 1508 Cov.: 32 AF XY: 0.126 AC XY: 9393 AN XY: 74400

African (AFR) AF: 0.0852 AC: 3540 AN: 41530

American (AMR) AF: 0.116 AC: 1778 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 455 AN: 3470

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0509 AC: 245 AN: 4818

European-Finnish (FIN) AF: 0.132 AC: 1397 AN: 10586

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11929 AN: 67998

Other (OTH) AF: 0.125 AC: 265 AN: 2116

Alfa AF: 0.154 Hom.: 6004

Bravo AF: 0.129

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.8
DANN	Benign	0.49
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1480597; hg19: chr10-45161109;