4-109878941-A-G

Variant names:

• chr4-109878941-A-G
• rs6847149
• ENST00000737086.1:n.174+8036T>C

Variant summary

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

The ENST00000737086.1(ENSG00000296171):​n.174+8036T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 246,234 control chromosomes in the GnomAD database, including 77,621 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 0.82 (51027 hom., cov: 31)
  • Exomes 𝑓: 0.75 (26594 hom.)
• Consequence: ENSG00000296171 ENST00000737086.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 12 publications found

Genes affected

ENSG00000296171 (HGNC:):

KRT19P3 (HGNC:33424): (keratin 19 pseudogene 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000737086.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296171	ENST00000737086.1		n.174+8036T>C		intron	N/A
	KRT19P3	ENST00000507547.2	TSL:6	n.*129T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124023 AN: 151962 Hom.: 50982 Cov.: 31

Gnomad AFR AF: 0.922

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.777

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.791

GnomAD4 exome AF: 0.746 AC: 70205 AN: 94154 Hom.: 26594 AF XY: 0.738 AC XY: 36446 AN XY: 49388

African (AFR) AF: 0.907 AC: 2568 AN: 2832

American (AMR) AF: 0.641 AC: 4681 AN: 7298

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 1564 AN: 2046

East Asian (EAS) AF: 0.707 AC: 3683 AN: 5206

South Asian (SAS) AF: 0.682 AC: 9488 AN: 13906

European-Finnish (FIN) AF: 0.755 AC: 3103 AN: 4110

Middle Eastern (MID) AF: 0.732 AC: 265 AN: 362

European-Non Finnish (NFE) AF: 0.770 AC: 40951 AN: 53188

Other (OTH) AF: 0.750 AC: 3902 AN: 5206

GnomAD4 genome AF: 0.816 AC: 124121 AN: 152080 Hom.: 51027 Cov.: 31 AF XY: 0.812 AC XY: 60330 AN XY: 74330

African (AFR) AF: 0.922 AC: 38245 AN: 41488

American (AMR) AF: 0.706 AC: 10790 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2748 AN: 3470

East Asian (EAS) AF: 0.736 AC: 3792 AN: 5154

South Asian (SAS) AF: 0.702 AC: 3381 AN: 4814

European-Finnish (FIN) AF: 0.783 AC: 8275 AN: 10568

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.799 AC: 54300 AN: 67988

Other (OTH) AF: 0.794 AC: 1676 AN: 2112

Alfa AF: 0.814 Hom.: 33629

Bravo AF: 0.816

Asia WGS AF: 0.722 AC: 2510 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.56
DANN	Benign	0.33
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6847149;

hg19: chr4-110800097;