chr6-160912905-G-C

Variant names:

• chr6-160912905-G-C
• rs1247318
• ENST00000405580.2:n.440-576G>C

Variant summary

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

The ENST00000405580.2(ENSG00000220913):​n.440-576G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,094 control chromosomes in the GnomAD database, including 2,409 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 0.17 (2409 hom., cov: 32)
• Consequence: ENSG00000220913 ENST00000405580.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 4 publications found

Genes affected

ENSG00000220913 (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 (AFR) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000405580.2. 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
	ENSG00000220913	ENST00000405580.2	TSL:6	n.440-576G>C		intron	N/A
	ENSG00000224371	ENST00000413062.2	TSL:3	n.521+2874C>G		intron	N/A
	ENSG00000224371	ENST00000437861.2	TSL:5	n.510+2874C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26572 AN: 151976 Hom.: 2406 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.175 AC: 26590 AN: 152094 Hom.: 2409 Cov.: 32 AF XY: 0.179 AC XY: 13313 AN XY: 74356

African (AFR) AF: 0.197 AC: 8193 AN: 41500

American (AMR) AF: 0.142 AC: 2172 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3466

East Asian (EAS) AF: 0.181 AC: 932 AN: 5162

South Asian (SAS) AF: 0.158 AC: 763 AN: 4820

European-Finnish (FIN) AF: 0.258 AC: 2724 AN: 10564

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10689 AN: 67986

Other (OTH) AF: 0.171 AC: 360 AN: 2106

Alfa AF: 0.172 Hom.: 280

Bravo AF: 0.166

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.55
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs1247318; hg19: chr6-161333937;