rs2214310

Positions:

• chr7-25339244-G-A
• chr7-25339244-G-T

Variant summary

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

The XR_927105.2(LOC105375195):​n.890+7779G>A 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 0.551 in 152,088 control chromosomes in the GnomAD database, including 23,502 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 0.55 (23502 hom., cov: 33)
• Consequence: LOC105375195 XR_927105.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

LOC105375195 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375195	XR_927105.2	n.890+7779G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83737 AN: 151970 Hom.: 23483 Cov.: 33

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.551 AC: 83802 AN: 152088 Hom.: 23502 Cov.: 33 AF XY: 0.549 AC XY: 40775 AN XY: 74324

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.533

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.567

Alfa AF: 0.530 Hom.: 3783

Bravo AF: 0.564

Asia WGS AF: 0.489 AC: 1703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.80
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2214310; hg19: chr7-25378863;