rs7712023

Variant names:

• chr5-163462952-A-T
• rs7712023
• NM_001142556.2:c.47-904A>T

Variant summary

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

The NM_001142556.2(HMMR):​c.47-904A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,710 control chromosomes in the GnomAD database, including 13,281 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 0.41 (13281 hom., cov: 31)
• Consequence: HMMR NM_001142556.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 4 publications found

Genes affected

HMMR (HGNC:5012): (hyaluronan mediated motility receptor) The protein encoded by this gene is involved in cell motility. It is expressed in breast tissue and together with other proteins, it forms a complex with BRCA1 and BRCA2, thus is potentially associated with higher risk of breast cancer. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HMMR	NM_001142556.2	c.47-904A>T		intron_variant	Intron 1 of 17	ENST00000393915.9	NP_001136028.1
HMMR	NM_012484.3	c.47-904A>T		intron_variant	Intron 1 of 17		NP_036616.2
HMMR	NM_012485.3	c.47-904A>T		intron_variant	Intron 1 of 16		NP_036617.2
HMMR	NM_001142557.2	c.12+2214A>T		intron_variant	Intron 1 of 14		NP_001136029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HMMR	ENST00000393915.9	c.47-904A>T		intron_variant	Intron 1 of 17	1	NM_001142556.2	ENSP00000377492.4
HMMR	ENST00000520345.5	c.-251-904A>T		intron_variant	Intron 1 of 5	2		ENSP00000428481.1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62060 AN: 151594 Hom.: 13279 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.409 AC: 62074 AN: 151710 Hom.: 13281 Cov.: 31 AF XY: 0.404 AC XY: 29907 AN XY: 74098

African (AFR) AF: 0.305 AC: 12615 AN: 41360

American (AMR) AF: 0.445 AC: 6780 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3470

East Asian (EAS) AF: 0.183 AC: 944 AN: 5172

South Asian (SAS) AF: 0.283 AC: 1361 AN: 4810

European-Finnish (FIN) AF: 0.430 AC: 4494 AN: 10460

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.487 AC: 33055 AN: 67912

Other (OTH) AF: 0.430 AC: 903 AN: 2100

Alfa AF: 0.452 Hom.: 2149

Bravo AF: 0.409

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.47
PhyloP100		0.027
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7712023; hg19: chr5-162889958;