chr1-160647341-T-A

Variant names:

• chr1-160647341-T-A
• rs2295614
• ENST00000840727.1:n.50+6T>A

Variant summary

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

The ENST00000840727.1(ENSG00000228863):​n.50+6T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0953 in 176,178 control chromosomes in the GnomAD database, including 1,132 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 0.095 (929 hom., cov: 31)
  • Exomes 𝑓: 0.099 (203 hom.)
• Consequence: ENSG00000228863 ENST00000840727.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 8 publications found

Genes affected

ENSG00000228863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840727.1. 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
	ENSG00000228863	ENST00000840727.1		n.50+6T>A		splice_region intron	N/A
	ENSG00000228863	ENST00000840728.1		n.302+6T>A		splice_region intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0946 AC: 14378 AN: 151996 Hom.: 928 Cov.: 31

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0933

GnomAD4 exome AF: 0.0991 AC: 2384 AN: 24064 Hom.: 203 Cov.: 0 AF XY: 0.0982 AC XY: 1234 AN XY: 12562

African (AFR) AF: 0.0660 AC: 82 AN: 1242

American (AMR) AF: 0.100 AC: 288 AN: 2878

Ashkenazi Jewish (ASJ) AF: 0.0269 AC: 12 AN: 446

East Asian (EAS) AF: 0.329 AC: 693 AN: 2108

South Asian (SAS) AF: 0.0854 AC: 253 AN: 2962

European-Finnish (FIN) AF: 0.116 AC: 76 AN: 658

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 68

European-Non Finnish (NFE) AF: 0.0705 AC: 891 AN: 12630

Other (OTH) AF: 0.0830 AC: 89 AN: 1072

GnomAD4 genome AF: 0.0947 AC: 14399 AN: 152114 Hom.: 929 Cov.: 31 AF XY: 0.0985 AC XY: 7326 AN XY: 74384

African (AFR) AF: 0.0942 AC: 3909 AN: 41500

American (AMR) AF: 0.105 AC: 1610 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0294 AC: 102 AN: 3466

East Asian (EAS) AF: 0.366 AC: 1887 AN: 5160

South Asian (SAS) AF: 0.0965 AC: 466 AN: 4828

European-Finnish (FIN) AF: 0.133 AC: 1405 AN: 10590

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4807 AN: 67978

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.0400 Hom.: 29

Bravo AF: 0.0926

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.2
DANN	Benign	0.81
PhyloP100		0.13
PromoterAI		0.033	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2295614; hg19: chr1-160617131;