6-163768869-C-T

Variant names:

• chr6-163768869-C-T
• rs4055434
• ENST00000657138.2:n.389+9440C>T

Variant summary

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

The ENST00000657138.2(ENSG00000235538):​n.389+9440C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.895 in 152,008 control chromosomes in the GnomAD database, including 61,028 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 0.90 (61028 hom., cov: 32)
• Consequence: ENSG00000235538 ENST00000657138.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 2 publications found

Genes affected

ENSG00000235538 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657138.2. 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
	ENSG00000235538	ENST00000657138.2		n.389+9440C>T		intron	N/A
	ENSG00000235538	ENST00000657157.2		n.375-4272C>T		intron	N/A
	ENSG00000235538	ENST00000657614.1		n.330-4272C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136001 AN: 151890 Hom.: 60970 Cov.: 32

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.895 AC: 136118 AN: 152008 Hom.: 61028 Cov.: 32 AF XY: 0.891 AC XY: 66163 AN XY: 74282

African (AFR) AF: 0.888 AC: 36862 AN: 41528

American (AMR) AF: 0.933 AC: 14261 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3195 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5111 AN: 5188

South Asian (SAS) AF: 0.901 AC: 4338 AN: 4816

European-Finnish (FIN) AF: 0.775 AC: 8153 AN: 10514

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61215 AN: 67892

Other (OTH) AF: 0.915 AC: 1928 AN: 2108

Alfa AF: 0.897 Hom.: 25992

Bravo AF: 0.907

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.083
DANN	Benign	0.25
PhyloP100		-0.78

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: rs4055434;

hg19: chr6-164189901;