rs1256120

Positions:

• chr14-64338283-A-G
• chr14-64338283-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000359491.1(ENSG00000214770):​n.317T>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 0.197 in 155,434 control chromosomes in the GnomAD database, including 3,602 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 0.20 (3564 hom., cov: 32)
  • Exomes 𝑓: 0.13 (38 hom.)
• Consequence: ENST00000359491.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESR2	NM_001291712.2	c.-1461T>C		5_prime_UTR_variant	1/14
ESR2	NM_001291723.1	c.-476T>C		5_prime_UTR_variant	1/9
ESR2	XM_047431076.1	c.-784T>C		5_prime_UTR_variant	1/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000359491.1	n.317T>C		non_coding_transcript_exon_variant	1/3	1
	ENST00000648279.1	n.357T>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30089 AN: 151928 Hom.: 3550 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.132 AC: 447 AN: 3388 Hom.: 38 Cov.: 0 AF XY: 0.144 AC XY: 278 AN XY: 1924

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.313

Gnomad4 ASJ exome AF: 0.100

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.111

Gnomad4 FIN exome AF: 0.180

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.209

GnomAD4 genome AF: 0.198 AC: 30151 AN: 152046 Hom.: 3564 Cov.: 32 AF XY: 0.199 AC XY: 14782 AN XY: 74330

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.0966

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.187

Alfa AF: 0.176 Hom.: 354

Bravo AF: 0.210

Asia WGS AF: 0.263 AC: 915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1256120; hg19: chr14-64805001; COSMIC: COSV104421842;