4-164987569-A-G

Variant names:

• chr4-164987569-A-G
• rs4691139
• ENST00000510050.1:n.305A>G

Variant summary

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

The ENST00000510050.1(ENSG00000248229):​n.305A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 152,108 control chromosomes in the GnomAD database, including 23,091 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 0.54 (23048 hom., cov: 31)
  • Exomes 𝑓: 0.54 (43 hom.)
• Consequence: ENSG00000248229 ENST00000510050.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 23 publications found

Genes affected

ENSG00000248229 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510050.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248229	ENST00000510050.1	TSL:6	n.305A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000298155	ENST00000753407.1		n.233-2350A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82152 AN: 151700 Hom.: 23003 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.538 AC: 156 AN: 290 Hom.: 43 Cov.: 0 AF XY: 0.532 AC XY: 84 AN XY: 158

African (AFR) AF: 0.750 AC: 3 AN: 4

American (AMR) AF: 0.750 AC: 6 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 7 AN: 14

East Asian (EAS) AF: 0.706 AC: 24 AN: 34

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.400 AC: 12 AN: 30

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.516 AC: 95 AN: 184

Other (OTH) AF: 0.563 AC: 9 AN: 16

GnomAD4 genome AF: 0.542 AC: 82257 AN: 151818 Hom.: 23048 Cov.: 31 AF XY: 0.542 AC XY: 40172 AN XY: 74164

African (AFR) AF: 0.652 AC: 26994 AN: 41406

American (AMR) AF: 0.594 AC: 9058 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2066 AN: 3472

East Asian (EAS) AF: 0.717 AC: 3680 AN: 5136

South Asian (SAS) AF: 0.664 AC: 3191 AN: 4808

European-Finnish (FIN) AF: 0.370 AC: 3888 AN: 10516

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.465 AC: 31560 AN: 67924

Other (OTH) AF: 0.569 AC: 1197 AN: 2102

Alfa AF: 0.503 Hom.: 87009

Bravo AF: 0.564

Asia WGS AF: 0.725 AC: 2523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.62
DANN	Benign	0.20
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4691139; hg19: chr4-165908721;