1-206503888-T-G

Variant names:

• chr1-206503888-T-G
• rs2871360
• XR_007066830.1:n.1775A>C

Variant summary

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

The XR_007066830.1(LOC124904493):​n.1775A>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 0.393 in 152,050 control chromosomes in the GnomAD database, including 12,690 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 0.39 (12689 hom., cov: 32)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: LOC124904493 XR_007066830.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 7 publications found

Genes affected

LOC124904493 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562504.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261000	ENST00000562504.1	TSL:6	n.-60T>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59697 AN: 151926 Hom.: 12689 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.399

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

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) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.393 AC: 59731 AN: 152044 Hom.: 12689 Cov.: 32 AF XY: 0.391 AC XY: 29028 AN XY: 74312

African (AFR) AF: 0.232 AC: 9628 AN: 41466

American (AMR) AF: 0.431 AC: 6591 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3468

East Asian (EAS) AF: 0.375 AC: 1945 AN: 5180

South Asian (SAS) AF: 0.566 AC: 2727 AN: 4818

European-Finnish (FIN) AF: 0.392 AC: 4133 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31834 AN: 67962

Other (OTH) AF: 0.395 AC: 833 AN: 2110

Alfa AF: 0.423 Hom.: 2350

Bravo AF: 0.384

Asia WGS AF: 0.438 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.28
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2871360; hg19: chr1-206677221;