chr4-162816969-C-G

Variant names:

• chr4-162816969-C-G
• rs6840361
• ENST00000661387.1:n.165+75190C>G

Variant summary

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

The ENST00000661387.1(ENSG00000248431):​n.165+75190C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,804 control chromosomes in the GnomAD database, including 1,196 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 0.11 (1196 hom., cov: 32)
• Consequence: ENSG00000248431 ENST00000661387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 4 publications found

Genes affected

ENSG00000248431 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661387.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248431	ENST00000661387.1		n.165+75190C>G		intron	N/A
	ENSG00000287072	ENST00000662873.1		n.157+3901G>C		intron	N/A
	ENSG00000248431	ENST00000728266.1		n.186-40040C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16649 AN: 151688 Hom.: 1188 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.0803

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.0725

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.110 AC: 16681 AN: 151804 Hom.: 1196 Cov.: 32 AF XY: 0.107 AC XY: 7938 AN XY: 74184

African (AFR) AF: 0.204 AC: 8445 AN: 41368

American (AMR) AF: 0.0802 AC: 1223 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 463 AN: 3468

East Asian (EAS) AF: 0.0847 AC: 437 AN: 5162

South Asian (SAS) AF: 0.111 AC: 536 AN: 4812

European-Finnish (FIN) AF: 0.0271 AC: 284 AN: 10490

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0724 AC: 4921 AN: 67948

Other (OTH) AF: 0.103 AC: 216 AN: 2098

Alfa AF: 0.0898 Hom.: 113

Bravo AF: 0.117

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs6840361; hg19: chr4-163738121;