rs4072169

Positions:

• chr4-157980512-G-A
• chr4-157980512-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660468.1(ENSG00000287226):​n.769+7194C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,140 control chromosomes in the GnomAD database, including 5,516 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 0.24 (5516 hom., cov: 33)
• Consequence: ENST00000660468.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377509	XR_007058347.1	n.291+7194C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000660468.1	n.769+7194C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36208 AN: 152022 Hom.: 5498 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.238 AC: 36233 AN: 152140 Hom.: 5516 Cov.: 33 AF XY: 0.246 AC XY: 18306 AN XY: 74388

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.312

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.235

Alfa AF: 0.224 Hom.: 1129

Bravo AF: 0.243

Asia WGS AF: 0.576 AC: 1998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4072169; hg19: chr4-158901664;