rs2790645

Positions:

• chr1-239251459-A-G

Variant summary

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

The XR_949313.2(LOC105373223):​n.571-516T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,014 control chromosomes in the GnomAD database, including 5,498 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 0.23 (5498 hom., cov: 32)
• Consequence: LOC105373223 XR_949313.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

Genes affected

LOC105373223 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373223	XR_949313.2	n.571-516T>C		intron_variant, non_coding_transcript_variant
LOC105373223	XR_949314.2	n.684-516T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35365 AN: 151896 Hom.: 5494 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0701

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.225

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.233 AC: 35397 AN: 152014 Hom.: 5498 Cov.: 32 AF XY: 0.229 AC XY: 17019 AN XY: 74326

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.0704

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.223

Alfa AF: 0.171 Hom.: 2290

Bravo AF: 0.246

Asia WGS AF: 0.109 AC: 380 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.18
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2790645; hg19: chr1-239414759;