7-76322895-G-T

Variant names:

• chr7-76322895-G-T
• rs2961037
• ENST00000803640.1:n.249-2001G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000803640.1(FPASL):​n.249-2001G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,076 control chromosomes in the GnomAD database, including 33,564 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 0.65 (33564 hom., cov: 32)
• Consequence: FPASL ENST00000803640.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 4 publications found

Genes affected

FPASL (HGNC:56688): (fibroblast proliferation associated lncRNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 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
FPASL	ENST00000803640.1	n.249-2001G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98196 AN: 151958 Hom.: 33516 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.646 AC: 98301 AN: 152076 Hom.: 33564 Cov.: 32 AF XY: 0.649 AC XY: 48266 AN XY: 74318

African (AFR) AF: 0.858 AC: 35600 AN: 41488

American (AMR) AF: 0.639 AC: 9757 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1727 AN: 3460

East Asian (EAS) AF: 0.937 AC: 4844 AN: 5172

South Asian (SAS) AF: 0.600 AC: 2890 AN: 4816

European-Finnish (FIN) AF: 0.597 AC: 6315 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.520 AC: 35375 AN: 67984

Other (OTH) AF: 0.602 AC: 1272 AN: 2112

Alfa AF: 0.600 Hom.: 3710

Bravo AF: 0.664

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.61
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs2961037; hg19: chr7-75952212;