rs34974495

Positions:

• chr18-60373556-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000658928.1(ENSG00000285681):​n.156+44211G>A 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 0.0149 in 149,920 control chromosomes in the GnomAD database, including 13 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 0.015 (13 hom., cov: 32)
• Consequence: ENST00000658928.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0149 (2241/149920) while in subpopulation SAS AF= 0.0243 (116/4766). AF 95% confidence interval is 0.0207. There are 13 homozygotes in gnomad4. There are 1056 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 13 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000658928.1	n.156+44211G>A		intron_variant, non_coding_transcript_variant
	ENST00000650201.1	n.113+44211G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0150 AC: 2240 AN: 149808 Hom.: 13 Cov.: 32

Gnomad AFR AF: 0.0158

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00532

Gnomad ASJ AF: 0.00289

Gnomad EAS AF: 0.00156

Gnomad SAS AF: 0.0251

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.00968

Gnomad NFE AF: 0.0182

Gnomad OTH AF: 0.0106

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

GnomAD4 genome AF: 0.0149 AC: 2241 AN: 149920 Hom.: 13 Cov.: 32 AF XY: 0.0145 AC XY: 1056 AN XY: 72980

Gnomad4 AFR AF: 0.0159

Gnomad4 AMR AF: 0.00531

Gnomad4 ASJ AF: 0.00289

Gnomad4 EAS AF: 0.00156

Gnomad4 SAS AF: 0.0243

Gnomad4 FIN AF: 0.0125

Gnomad4 NFE AF: 0.0182

Gnomad4 OTH AF: 0.0105

Alfa AF: 0.0176 Hom.: 4

Bravo AF: 0.0140

Asia WGS AF: 0.00781 AC: 27 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34974495; hg19: chr18-58040789;