rs4619440

Variant names:

• chr17-65491282-C-T
• rs4619440

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 0.161 in 152,034 control chromosomes in the GnomAD database, including 3,177 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 0.16 (3177 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 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: 0.161 AC: 24463 AN: 151914 Hom.: 3148 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.161 AC: 24535 AN: 152034 Hom.: 3177 Cov.: 32 AF XY: 0.163 AC XY: 12092 AN XY: 74344

African (AFR) AF: 0.324 AC: 13431 AN: 41402

American (AMR) AF: 0.104 AC: 1591 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3472

East Asian (EAS) AF: 0.408 AC: 2095 AN: 5132

South Asian (SAS) AF: 0.142 AC: 685 AN: 4814

European-Finnish (FIN) AF: 0.126 AC: 1335 AN: 10600

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4730 AN: 68008

Other (OTH) AF: 0.139 AC: 294 AN: 2112

Alfa AF: 0.109 Hom.: 240

Bravo AF: 0.171

Asia WGS AF: 0.287 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.60
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs4619440; hg19: chr17-63487400;