chr4-189979962-A-G

Variant names:

• chr4-189979962-A-G
• rs10005101
• ENST00000604941.3:n.61A>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000604941.3(ENSG00000271307):​n.61A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.60 (13498 hom., cov: 44)
  • Exomes 𝑓: 0.60 (160 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000271307 ENST00000604941.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• Publications: 1 publications found

Genes affected

ENSG00000271307 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000604941.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000271307	ENST00000604941.3	TSL:6	n.61A>G		non_coding_transcript_exon	Exon 1 of 6

Frequencies

GnomAD3 genomes AF: 0.599 AC: 77561 AN: 129586 Hom.: 13477 Cov.: 44

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.580

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.590

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.598 AC: 941 AN: 1574 Hom.: 160 Cov.: 0 AF XY: 0.598 AC XY: 665 AN XY: 1112

African (AFR) AF: 0.625 AC: 15 AN: 24

American (AMR) AF: 0.500 AC: 7 AN: 14

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 10 AN: 18

East Asian (EAS) AF: 0.583 AC: 14 AN: 24

South Asian (SAS) AF: 0.571 AC: 16 AN: 28

European-Finnish (FIN) AF: 0.597 AC: 74 AN: 124

Middle Eastern (MID) AF: 0.667 AC: 12 AN: 18

European-Non Finnish (NFE) AF: 0.595 AC: 711 AN: 1194

Other (OTH) AF: 0.631 AC: 82 AN: 130

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.599 AC: 77630 AN: 129682 Hom.: 13498 Cov.: 44 AF XY: 0.598 AC XY: 37911 AN XY: 63428

African (AFR) AF: 0.682 AC: 26391 AN: 38676

American (AMR) AF: 0.556 AC: 6827 AN: 12284

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 1715 AN: 2898

East Asian (EAS) AF: 0.579 AC: 2534 AN: 4376

South Asian (SAS) AF: 0.580 AC: 2388 AN: 4120

European-Finnish (FIN) AF: 0.555 AC: 4828 AN: 8696

Middle Eastern (MID) AF: 0.637 AC: 163 AN: 256

European-Non Finnish (NFE) AF: 0.561 AC: 31289 AN: 55816

Other (OTH) AF: 0.591 AC: 1067 AN: 1804

Alfa AF: 0.569 Hom.: 1206

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	11
DANN	Benign	0.40
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10005101; hg19: chr4-190901117;