rs1978231

Variant names:

• chr4-109877437-T-A
• rs1978231
• ENST00000737086.1:n.174+9540A>T

Your query was ambiguous. Multiple possible variants found:

• chr4-109877437-T-A
• chr4-109877437-T-C
• chr4-109877437-T-G

Variant summary

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

The ENST00000737086.1(ENSG00000296171):​n.174+9540A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,064 control chromosomes in the GnomAD database, including 44,670 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 0.77 (44670 hom., cov: 31)
• Consequence: ENSG00000296171 ENST00000737086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410
• Publications: 1 publications found

Genes affected

ENSG00000296171 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.788 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
ENSG00000296171	ENST00000737086.1	n.174+9540A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116365 AN: 151946 Hom.: 44636 Cov.: 31

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.752

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.705

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.766 AC: 116443 AN: 152064 Hom.: 44670 Cov.: 31 AF XY: 0.761 AC XY: 56580 AN XY: 74310

African (AFR) AF: 0.795 AC: 32965 AN: 41464

American (AMR) AF: 0.674 AC: 10300 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2588 AN: 3472

East Asian (EAS) AF: 0.734 AC: 3784 AN: 5152

South Asian (SAS) AF: 0.705 AC: 3392 AN: 4812

European-Finnish (FIN) AF: 0.726 AC: 7665 AN: 10564

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.783 AC: 53275 AN: 67998

Other (OTH) AF: 0.751 AC: 1582 AN: 2106

Alfa AF: 0.688 Hom.: 1985

Bravo AF: 0.765

Asia WGS AF: 0.715 AC: 2486 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.73
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs1978231; hg19: chr4-110798593;