rs1247318

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378093	XR_943195.1	n.187+2874C>G		intron_variant	Intron 2 of 2
LOC105378093	XR_943196.1	n.162+2874C>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000220913	ENST00000405580.2	n.440-576G>C		intron_variant	Intron 3 of 3	6
ENSG00000224371	ENST00000413062.2	n.521+2874C>G		intron_variant	Intron 2 of 2	3
ENSG00000224371	ENST00000437861.2	n.510+2874C>G		intron_variant	Intron 2 of 3	5

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 v4.3

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;