rs927005

Variant names:

• chr14-65752364-G-A
• rs927005

Your query was ambiguous. Multiple possible variants found:

• chr14-65752364-G-A
• chr14-65752364-G-C
• chr14-65752364-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0121 in 151,950 control chromosomes in the GnomAD database, including 15 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 0.012 (15 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0121 (1834/151950) while in subpopulation SAS AF = 0.0243 (117/4818). AF 95% confidence interval is 0.0207. There are 15 homozygotes in GnomAd4. There are 889 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 15 gene

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: 0.0121 AC: 1837 AN: 151832 Hom.: 15 Cov.: 32

Gnomad AFR AF: 0.00349

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0155

Gnomad ASJ AF: 0.0259

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0241

Gnomad FIN AF: 0.00955

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0164

Gnomad OTH AF: 0.0120

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

GnomAD4 genome AF: 0.0121 AC: 1834 AN: 151950 Hom.: 15 Cov.: 32 AF XY: 0.0120 AC XY: 889 AN XY: 74278

African (AFR) AF: 0.00348 AC: 144 AN: 41434

American (AMR) AF: 0.0154 AC: 234 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.0243 AC: 117 AN: 4818

European-Finnish (FIN) AF: 0.00955 AC: 101 AN: 10578

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0164 AC: 1115 AN: 67952

Other (OTH) AF: 0.0119 AC: 25 AN: 2106

Alfa AF: 0.00234 Hom.: 7

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs927005; hg19: chr14-66219082;