rs2249612

Positions:

• chr7-113101879-G-A
• chr7-113101879-G-C
• chr7-113101879-G-T

Variant summary

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

The XM_047421162.1(LOC107986837):​c.67+994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,130 control chromosomes in the GnomAD database, including 53,490 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 0.84 (53490 hom., cov: 31)
• Consequence: LOC107986837 XM_047421162.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236

Genes affected

LOC107986837 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986837	XM_047421162.1	c.67+994G>A		intron_variant			XP_047277118.1
LOC107986837	XM_047421161.1	c.67+994G>A		intron_variant			XP_047277117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000441928.1	n.223+994G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.837 AC: 127258 AN: 152012 Hom.: 53430 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.841

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

GnomAD4 genome AF: 0.837 AC: 127369 AN: 152130 Hom.: 53490 Cov.: 31 AF XY: 0.837 AC XY: 62275 AN XY: 74384

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.901

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.871

Gnomad4 NFE AF: 0.821

Gnomad4 OTH AF: 0.843

Alfa AF: 0.822 Hom.: 10441

Bravo AF: 0.843

Asia WGS AF: 0.820 AC: 2848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2249612; hg19: chr7-112741934;