chr1-111432313-A-G

Variant names:

• chr1-111432313-A-G
• rs1264913
• ENST00000564771.1:n.756T>C

Variant summary

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

The ENST00000564771.1(ENSG00000260948):​n.756T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,178 control chromosomes in the GnomAD database, including 1,390 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 0.12 (1390 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000260948 ENST00000564771.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 8 publications found

Genes affected

ENSG00000260948 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260948	ENST00000564771.1	n.756T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17855 AN: 152060 Hom.: 1393 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0840

Gnomad OTH AF: 0.128

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.117 AC: 17858 AN: 152178 Hom.: 1390 Cov.: 32 AF XY: 0.123 AC XY: 9125 AN XY: 74400

African (AFR) AF: 0.122 AC: 5062 AN: 41510

American (AMR) AF: 0.110 AC: 1682 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0893 AC: 310 AN: 3470

East Asian (EAS) AF: 0.436 AC: 2257 AN: 5174

South Asian (SAS) AF: 0.213 AC: 1031 AN: 4830

European-Finnish (FIN) AF: 0.141 AC: 1489 AN: 10590

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0840 AC: 5711 AN: 67996

Other (OTH) AF: 0.129 AC: 272 AN: 2114

Alfa AF: 0.0991 Hom.: 288

Bravo AF: 0.118

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.64
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs1264913; hg19: chr1-111974935;