rs11971770

Variant names:

• chr7-150562663-A-G
• rs11971770
• XM_017012936.2:c.571+550T>C

Variant summary

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

The XM_017012936.2(LOC107986860):​c.571+550T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 152,050 control chromosomes in the GnomAD database, including 10,836 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 0.34 (10836 hom., cov: 32)
• Consequence: LOC107986860 XM_017012936.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 2 publications found

Genes affected

LOC107986860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986860	XM_017012936.2	c.571+550T>C		intron_variant	Intron 1 of 1		XP_016868425.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51658 AN: 151932 Hom.: 10802 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.340 AC: 51747 AN: 152050 Hom.: 10836 Cov.: 32 AF XY: 0.343 AC XY: 25471 AN XY: 74342

African (AFR) AF: 0.596 AC: 24690 AN: 41452

American (AMR) AF: 0.264 AC: 4026 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 831 AN: 3470

East Asian (EAS) AF: 0.365 AC: 1884 AN: 5168

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4826

European-Finnish (FIN) AF: 0.239 AC: 2527 AN: 10584

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15011 AN: 67954

Other (OTH) AF: 0.302 AC: 638 AN: 2114

Alfa AF: 0.297 Hom.: 1365

Bravo AF: 0.350

Asia WGS AF: 0.380 AC: 1318 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.23
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs11971770; hg19: chr7-150259751;